Mitochondria analytics
Visualization and analysis tools for analyzing mitochondria in the Layer 2/3 EM volume
visualize all mitochondria in a cell of interest
Contents
Visualization tools
Visualize a single mitochondrion of interest in Neuroglancer
neuroglancer_link_generator_mitochondria_visualization_version.ipynb:
generate a Neuroglancer link for a single cellid and single
mitochondrion from the
pni_mito_cellswskel_v185_fullstats.csv datatable. The view
will be centered at the centroid of the mitochondrion in the volume.
neuroglancer link to a single mitochondrion with crosshair at the mito centroid
Visualize all mitochondria in a neuron of interest in Neuroglancer
neuroglancer_link_generator_all_mitochondria.ipynb:
generate a Neuroglancer link for all the mitochondria in a single cellid
of interest pulling the mito ids from the
211019_mitochondria_info.csv datatable.
neuroglancer link generator for all mitochondria in a cell
Visualize neuronal mitochondria by compartment in Neuroglancer
neuroglancer_link_generator_neuronalmitochondria_bycompartment.ipynb:
as above, but allows to select for a compartment of interest. Neuronal
compartment assignments are based on the method described by
Reconstruction of neocortex: Organelles, compartments, cells,
circuits, and activity Turner
et al, Cell 2022.
neuroglancer link generator for mitochondria by compartment
3D visualizer of all mitochondria in a cell of interesting using Meshparty, vtk, and OpenGL viewer
vtk_mitochondria_visualizer.ipynb:
generate a 3D interactive view of all mitochondria in a cell of
interest. Note this method has significant file download and space
requirements compared to using the Neuroglancer viewer.
3D visualizer of all mitochondria in a cell
3D visualizer of all mitochondria and synapses in a cell of interesting using Meshparty, vtk, and OpenGL viewer
vtk_mitochondria_visualizer_with_synapses.ipynb:
generate a 3D interactive view of all mitochondria in a cell of interest
along with the pre- and post-syanptic sites. Note this method has
significant file download and space requirements compared to using the
Neuroglancer viewer.
3D visualizer of all mitochondria and synapses in a cell
3D vector plots by cellid lookup by neuronal subtype
mitochondria_3d_vector_plots_by_cellid_lookup_by_neuronal_subtype.ipynb:
generate 3D interactive scatterplots in Plotly, 3D quiver plots in
matplotlib, and a Neuroglancer views with this notebook. Uses a
dataframe that generates spatial and vector calculations from the
original mitochondria dataframe by Turner et al. Download
mito_above_soma.csv in the data
folder.
3D quiver plot of mito centroid with bounding box distance vector
3D visualization for mitochondria within a 45 degree cone above soma
3dvisualizer_for_withincone.ipynb:
generate 3D interactive scatterplots in Plotly, 3D quiver plots in
matplotlib, and Neuroglancer views with this notebook. Uses a dataframe
that generates spatial, vector, and cone angle calculations from the
original mitochondria dataframe by Turner et al. Download
pyr_all.csv in the data
folder. Special thanks to Qiao Liu and Wanwen Zeng at Stanford for
their assistance in debugging the code.
3D scatterplot using Plotly for visualizing mitochondria within a 45 degree cone above soma